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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcagagccgtgatgttttctatttcatttacttaagcttctttgatttctattaatctaaactttctttcatttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTAC

Basic information

species Glycine max
transcript GLYMA13G36230.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G36230.2 (Glycine max), 3'ss of exon 15
lower sequence: AT5G54670.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatgcagagccgtgatgttttctatttcatttacttaagcttctttgatttctattaatctaaactttctttcatttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTAC
||| |       |  |       ||   |||     |    |  |   |||| || |    ||||||||| ||| ||     | ||||||| || |||||| |||| ||  || | ||||| ||||| ||||| || ||||| || |||||| | |||||| | ||||||||||||||||| || |
gtacgtttgatagaaaca-----taaaacatgattatggtttcttgcaatttttagtctcttaaactttcattctttc---ttcagGCAATCAACAAAAGTTTGTCGTCGCTAGGCGATGTCATATTCGCCTTAGCAAAGAAAGAAGATCATGTACCATTCCGAAACTCAAAGCTCACATATCTTC

upper sequence: GLYMA13G36230.2 (Glycine max), 3'ss of exon 15
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 3'ss of exon 14
---------gtatgcagagccgtgatgttttctatttcatttacttaagcttctttgatttc-tattaatctaaactttctttcatttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTAC
           |  | ||  |  | |   |||| ||   ||||||||   || |     ||  |||| || || | | | ||||| || | |  |||| || ||||| ||||||||||||||||||||||| ||||||||| |||| ||||||||||| ||| | ||||| |||||||||||||| || || || |
gtatttgagaaacactgatacaagcttaattctgttaattttacttatcattatgcatctttatatttatatatattct-tttcaattatgac-agGCCATCAATAAGAGTCTGTCATCATTAAGTGATGTTATATTTGCCCTGGCAAAGAAGGAGGACCATGTACCATTTAGGAACTCAAAGCTTACGTATCTTC
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|208218829|gb|GE016147.1|GE016147
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|193542299|gb|FK497517.1|FK497517
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGGGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|207687107|gb|GD669795.1|GD669795
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCC
EST: gi|193306454|gb|FK273379.1|FK273379
EST:     AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAA                         GCAATAAATAAAAGTCTGTCATCATTAAG
genomic: AACGTCTTTCAAGGAGTGGATCAACCGGGGACCGATTGAAAGAGACTCAAgtatgcagag ... ttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacttaagcttctttgatttctattaatctaaactttctttcatttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTAC
                                  ctttctttcatttgt  CT-rich tract
             tttgatttctattaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcagagccgtgatgttttctatttcatttacttaagcttctttgatttctattaatctaaactttctttcatttgtaattagGCAATAAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA